Mercurial > repos > greg > kaks_analysis

comparison kaks_analysis.xml @ 29:c91e1673c8e7 draft

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Uploaded
author greg
date Mon, 01 May 2017 12:41:26 -0400
parents b807167c1e60
children 9b78e5c2a14e
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28:b807167c1e60 29:c91e1673c8e7
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206 **Options** 206 **Options**
207 207
208 * **Required** 208 * **Required**
209 209
210 - **Coding sequences for the first species** - coding sequence fasta file for for the first species either produced by the AssemblyPostProcessor tool or an external source selected from your history. 210 - **Coding sequences for the first species** - coding sequence fasta file for the first species either produced by the AssemblyPostProcessor tool or from an external source selected from your history.
211 - **Protein sequences for the first species** - corresponding protein sequence fasta files for the first species either produced by the AssemblyPostProcessor tool or an external source selected from your history. 211 - **Protein sequences for the first species** - corresponding protein sequence fasta files for the first species either produced by the AssemblyPostProcessor tool or from an external source selected from your history.
212 - **Type of sequence comparison** - pairwise sequence comparison to determine homolgous pairs. This can be either paralogous for self-species comparison or orthologous for cross-species comparison. Cross species comparision requires data selected for the second species. 212 - **Type of sequence comparison** - pairwise sequence comparison to determine homolgous pairs. This can be either paralogous for self-species comparison or orthologous for cross-species comparison. Cross-species comparision requires input for the second species.
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214 * **Optional** 214 * **Optional**
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216 - **Coding sequences for the second species** - coding sequence fasta file for for the second species either produced by the AssemblyPostProcessor tool or an external source selected from your history. Required only for orthologous comparison. 216 - **Coding sequences for the second species** - coding sequence fasta file for the second species either produced by the AssemblyPostProcessor tool or from an external source selected from your history. This option is required only for orthologous comparison.
217 - **Protein sequences for the second species** - corresponding protein sequence fasta files for the second species either produced by the AssemblyPostProcessor tool or an external source selected from your history. Required only for orthologous comparison. 217 - **Protein sequences for the second species** - corresponding protein sequence fasta files for the second species either produced by the AssemblyPostProcessor tool or from an external source selected from your history. This option is required only for orthologous comparison.
218 - **Alignment coverage configuration** - select 'Yes' to set the minimum allowable alignment coverage length between homologous pairs. PlantTribes uses global codon alignment match score to determine the pairwise alignment coverage. By default, the match score is set to 0.5 if 'No' is selected. 218 - **Alignment coverage configuration** - select 'Yes' to set the minimum allowable alignment coverage length between homologous pairs. PlantTribes uses global codon alignment match score to determine the pairwise alignment coverage. By default, the match score is set to 0.5 if 'No' is selected.
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220 - **match score** - number of base matches in a pairwise sequence alignment divided by the length of shorter sequence. Positions in the alignment corresponding to gaps are not considered. The score is restricted to the range 0.3 - 1.0. 220 - **match score** - number of base matches in a pairwise sequence alignment divided by the length of shorter sequence. Positions in the alignment corresponding to gaps are not considered. The score is restricted to the range 0.3 - 1.0.
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222 - **Species rates recalibration configuration** - select 'Yes' to recalibrate synonymous substitution rates of a species using a predetermined evolutionary rate. Recalibration evolutionary rate can be determined from a species tree inferred from a collection of conserved single copy genes from taxa of interest as described in Cui et al., 2006. Applies only to paralogous comparisons. 222 - **Species rates recalibration configuration** - select 'Yes' to recalibrate synonymous substitution rates of a species using a predetermined evolutionary rate. Recalibration evolutionary rate can be determined from a species tree inferred from a collection of conserved single copy genes from taxa of interest as described in Cui et al., 2006. Rate recalibration applies only to paralogous comparisons.
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224 - **recalibration rate** - a predetermined evolutionary recalibration rate. 224 - **recalibration rate** - a predetermined evolutionary recalibration rate.
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226 - **PAML codeml configuration** - select 'Yes' to enable selection of a PAML codeml control file to carry out maximum likelihood analysis of protein-coding DNA sequences using codon substitution models. Template file "codeml.ctl.args" can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and are also available at the PlantTribes GitHub `repository`_. Default settings shown in the template are used if 'No' is selected. 226 - **PAML codeml configuration** - select 'Yes' to enable selection of a PAML codeml control file to carry out maximum likelihood analysis of protein-coding DNA sequences using codon substitution models. Template file "codeml.ctl.args" can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and are also available at the PlantTribes GitHub `repository`_. Default settings shown in the template are used if 'No' is selected.
227 - **Rates clustering configuration** - select 'Yes' to estimate clusters of synonymous substitution rates using a mixture of multivariate normal distributions which represent putative duplication event(s). 227 - **Rates clustering configuration** - select 'Yes' to estimate clusters of synonymous substitution rates using a mixture of multivariate normal distributions which represent putative duplication event(s).